Plant Circular RNA Database

Detail information of 1_circ_ag.3

			
						 General Information
					
						CircRNA Name
						1_circ_ag.3
					
						ID in PlantcircBase
						ath_circ_002640
					
						Alias
						1:5221659-5225370
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 5221659-5225370  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							1_circ_ag.3 1_circ_ag.4 AT1G15165_circ_g.1 AT1G15165_circ_g.2 1_circ_ag.4 1_circ_ag.5 1_circ_ag.6 						
					
						Support reads
						1/1/1
					
						Tissues
						root;flower
					
						Exon boundary  
						
							NA-NA							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							GT-AG							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						NA

General Information
CircRNA Name	1_circ_ag.3
ID in PlantcircBase	ath_circ_002640
Alias	1:5221659-5225370
Organism	Arabidpsis thaliana
Position	chr1: 5221659-5225370 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	find_circ; CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	1_circ_ag.3 1_circ_ag.4 AT1G15165_circ_g.1 AT1G15165_circ_g.2 1_circ_ag.4 1_circ_ag.5 1_circ_ag.6
Support reads	1/1/1
Tissues	root;flower
Exon boundary	NA-NA "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	GT-AG The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	NA

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							CCTCTGCCTGTTCTGAGACACGCGCACCGCTCTCCATGGAGATATTTGACGGCATTGGAGAGTT
CTTCAGATATGCTCTTCCTTCTGCGGCTATGATTTGcctagagtggtggtcttatgaacttata
atattactctctggtctcttacccaacccacaactggagacttctgtgctctctgtctggtact
cctccttg

									
								

					

						Assembled circRNA sequence  
						
							NA
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							NA						
					

						Genomic sequence
						
							CCTAGAGTGGTGGTCTTATGAACTTATAATATTACTCTCTGGTCTCTTACCCAACCCACAACTG
GAGACTTCTGTGCTCTCTGTCTGGTACTCCTCCTTGCATCGATCAATTTCTTCTTGTTACAATT
TTGAATTTGCAAGAACATAATGTTATTCACACTGTGGCAGTCTTCAGACAATTTCAACAATGTA
TTCGATACCACTAGCAATCGCGGCTGCAGCAAGGTTAGAGCTTTAGTCACACTATGCAGTACAT
AAATACTGAAGCATATTTTCTGCTCATGACAAGGAATCATATGGTTTCATATTCATAAGCGGAT
GTTTATTTCTTGTGCAGCACAAGAATCTCAAATGAATTAGGTGCTGGAAACTCTCGAGCAGCAC
ATATCGTGGTCTATGCGGCAATGTCTCTTGCAGTTATTGATGCATTGATAGTTAGTATGTCTCT
ACTAATCGGCAGGAATCTTTTCGGGCACATTTTCAGCAGTGACAAGGAAACTATCGACTATGTT
GCAAAGATGGCTCCATTGGTCTCTATTTCTCTCATGCTTGACGCTTTACAAGGGGTCCTCTCAG
GTCTGAGACTTGTTCTTCTTTCTTTACTCACACACAAGTTCTTGTCGGATATTGTTTACTCTTT
TCCTCCACATAGTGCAAAGACACTTCATGTTCTGTGTTTTGTCCTGTGTCAAAAGCTATCCCAA
AAATATACTCTTTTCTACCACGCCTAATTGTCTTTTGATGGTTTGCAGGTATTGCAAGGGGATG
CGGATGGCAACATATAGGAGCTTACATAAACTTAGGAGCTTTCTATCTCTGGGGGATACCCATT
GCTGCATCTTTAGCCTTCTGGATTCATCTGAAAGGTGTTGGCCTTTGGATTGGAATCCAAGCCG
GTGCCGTTCTGCAAACGCTTCTGCTTGCTCTTGTCACGGGCTGTACAAACTGGGAAAGCCAGGT
CCTACTTCTTTTTCGTTCTTTTCTTCTTCATGACTAGTTTCTCTTGTGAAATAAACATACAGAT
CTTGAATTGGATGCATGTTTGAACTGTAGGCCGATAAAGCGAGGAATCGAATGGCTTTGGCCTA
TGGAACATAAGGCGCTGCAGAACAGCACTTACAGAATCAGATCTCCGCGTCTGAAGATATAGGG
ACCTGATGATCCTTCGGTTTTACCATTTTGTTAGTAGTCAAATTGCTGTACTGTATGTTACTTT
TGGACTAGTGGTAGCCGCAAGTAATATTGCATGGTTTTCCAAAAAGGAGCCTTTTCTCTGTTCT
CAACAACAAAGAATAATGAACAGATTCACTGGACTGTGAGCTTGACCATACAAGCAGAGACCAA
GAAGTGGTGGTATTGATGGAGCTGCTACAACCACCACATATCTCCAAATTGACAGCATCTGATT
TCCTGTCACTAGTCCCACTTCTCACAAGAGTAACTGAATTACTCGAACCTGTTAAAGTTATCAA
ACCAATTTTAATGATCAATCTTGGGGCAAGGCTTTAAAAGGCACCCTCAGTGTCAATTAGAAAC
ATAACATAGAGTTTCTACTGAGTCTTGGGGCAAGAGCTGTCCATCAGTGATACATTCCTCAATA
CAGACATGTTCATAAGTCTGTCCAGAAGCAAAAAATGATTACCTACTCTCCATGGGCTTATATA
GTTAATAGAACTAAACTTTGATAGTTGACACCAAATGCATGAACACGATCTTCATTAGAACCTT
GACCAGTGAGGGAACATGGTGTTGGACACTAAGAGTCATATATCATCCAAAATTCCACTTCAGA
ATAGAATGGAGTATTTTCTCATGAGGTATGACAAATAATTGATTCCTTCCGGTTGTCTTCTCCC
ACACGTGCCTTGTGAATGAGTTCTTTAAAGCACGTTGCTGTCACTGCAAGTTGTCAAATTTCGT
CAACTGTTGCAACCGTGCAATCATCCGATCACCAACTTCCTTCTCTGATATGGATCAAGCAACA
ATGTCCAAATCTGAACAAATCACATATCAAAATTAGAATTGCAACAAGGAACTACCAGAGACCA
ATTTATAAATTCAGAAGCAAATATACACGAGGGCATAATTAATCAAACTGGCTGCAAGAGACTT
ATAAACCCTGAACAGTTGCTAATATCGCATGGAGGACATTGTTGCTAGCTCAACTGGGTCTCAG
ATGATGTCTGTTTCAGTAAAAAGTAACACATAACTGCATTTTATCAATGGCCATAACACACAAC
TTTAACAAAGCATAGAGAACAAGACCATAAAAACATAAATTACATCAAAGAACAAGAACAGAAA
TCTAAAAACAAAGCAAGAAGGAGCGATCACACTTCAAATAAACCAATGAGGTAGTGGACAAAGC
CCTCACCTAATTCCAGATCAAACCGGCGGAGATGACGGGTGAGGGGAAGTCAGCGCAGGATAAA
CATGGGAGGGAGAGAGATAGTGGCTAAATTCCACATGGGTGACAGAGGGCGCCAAAGTATGACT
TACTTGGAGTGATTTGGATAGAAAATGGTGACACGTGGACACTCAAGATATCATTTTTATCTTT
TTCCCAACCACTTGTGAGCTGTGTAGGAGAGAAGTAATGAACATATAAGCAAAAACAAATGTTG
TTACAAAAACAAGTCCCCACCACATTTACTACTACTAGTTTGACAAACATAAACACATTTCCCT
TATTAACATTTCTTGTTAACCACACAAAGTTAATAAGTAACCCAAGTTTATACAGTTTTAAAAC
ATTCTCTCTATCTCCCTCCGGCTAGGCTGTAGCTGTTCGCCATGGGAGACGCAGAGAGCACCTC
CAAAACTAGCTTGCTGCTCCCGGTGGAAAGAGTTGAAAACGTGACATGGAGAGATCTGCGAGAT
GGATTATTCACCGCAGAACTCAAGAGGCTTATCTGCTTTGCCGCTCCTATGGCGGCTGTTGTTA
TCGCTCAGTTCATGTTGCAGATCATCTCAATGGTGATGGTTGGTCACCTCGGAAATCTCTCCCT
CGCTAGTGCCTCTCTCGCCTCCTCCTTCTGCAACGTCACCGGCTTCAGCTTCATCGTCTGTTTT
CTCTTCCTTCTCTCCTCTTTATCTCTATCTATTACTAGTTATCAAATTGCATCCCCTCATTACT
TGATTAGTTGATTGTTACTTTTTGATGCTAGGTAGGATTGTCATGTGCCTTAGATACTTTGAGT
GGTCAAGCTTATGGAGCTAAGCTATATCGGAAAGTAGGAGTTCAGACTTACACAGCAATGTTCT
GTCTTGCATTAGTATGTCTCCCTCTCACTCTCATATGGTTAAACATGGAAACGCTTCTTGTATT
CCTTGGCCAAGATCCTTCTATTGCTCACGAAGCCGGCAGATATGCTGCTTGCCTCATCCCAGGA
CTGTTTGCTTACGCTGTTCTACAGCCTCTCACTCGCTACTTCCAAAACCAGAGCATGATTACAC
CTCTCCTCATCACCTCTTGTTTTGTGTTCTGTCTCCATGTTCCTCTCTGCTGGCTTTTGGTTTA
TAAGTCAGGGCTTGGTAATCTTGGAGGAGCCTTAGCTCTCAGTTTTTCGAACTGTCTTTATACC
ATTATCCTTGGATCTTTAATGTGCTTCTCCTCTGCCTGTTCTGAGACACGCGCACCGCTCTCCA
TGGAGATATTTGACGGCATTGGAGAGTTCTTCAGATATGCTCTTCCTTCTGCGGCTATGATTTG
						
					

			
		

Sequences
Splice junction sequence	CCTCTGCCTGTTCTGAGACACGCGCACCGCTCTCCATGGAGATATTTGACGGCATTGGAGAGTT CTTCAGATATGCTCTTCCTTCTGCGGCTATGATTTGcctagagtggtggtcttatgaacttata atattactctctggtctcttacccaacccacaactggagacttctgtgctctctgtctggtact cctccttg
Assembled circRNA sequence	NA The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	NA
Genomic sequence	CCTAGAGTGGTGGTCTTATGAACTTATAATATTACTCTCTGGTCTCTTACCCAACCCACAACTG GAGACTTCTGTGCTCTCTGTCTGGTACTCCTCCTTGCATCGATCAATTTCTTCTTGTTACAATT TTGAATTTGCAAGAACATAATGTTATTCACACTGTGGCAGTCTTCAGACAATTTCAACAATGTA TTCGATACCACTAGCAATCGCGGCTGCAGCAAGGTTAGAGCTTTAGTCACACTATGCAGTACAT AAATACTGAAGCATATTTTCTGCTCATGACAAGGAATCATATGGTTTCATATTCATAAGCGGAT GTTTATTTCTTGTGCAGCACAAGAATCTCAAATGAATTAGGTGCTGGAAACTCTCGAGCAGCAC ATATCGTGGTCTATGCGGCAATGTCTCTTGCAGTTATTGATGCATTGATAGTTAGTATGTCTCT ACTAATCGGCAGGAATCTTTTCGGGCACATTTTCAGCAGTGACAAGGAAACTATCGACTATGTT GCAAAGATGGCTCCATTGGTCTCTATTTCTCTCATGCTTGACGCTTTACAAGGGGTCCTCTCAG GTCTGAGACTTGTTCTTCTTTCTTTACTCACACACAAGTTCTTGTCGGATATTGTTTACTCTTT TCCTCCACATAGTGCAAAGACACTTCATGTTCTGTGTTTTGTCCTGTGTCAAAAGCTATCCCAA AAATATACTCTTTTCTACCACGCCTAATTGTCTTTTGATGGTTTGCAGGTATTGCAAGGGGATG CGGATGGCAACATATAGGAGCTTACATAAACTTAGGAGCTTTCTATCTCTGGGGGATACCCATT GCTGCATCTTTAGCCTTCTGGATTCATCTGAAAGGTGTTGGCCTTTGGATTGGAATCCAAGCCG GTGCCGTTCTGCAAACGCTTCTGCTTGCTCTTGTCACGGGCTGTACAAACTGGGAAAGCCAGGT CCTACTTCTTTTTCGTTCTTTTCTTCTTCATGACTAGTTTCTCTTGTGAAATAAACATACAGAT CTTGAATTGGATGCATGTTTGAACTGTAGGCCGATAAAGCGAGGAATCGAATGGCTTTGGCCTA TGGAACATAAGGCGCTGCAGAACAGCACTTACAGAATCAGATCTCCGCGTCTGAAGATATAGGG ACCTGATGATCCTTCGGTTTTACCATTTTGTTAGTAGTCAAATTGCTGTACTGTATGTTACTTT TGGACTAGTGGTAGCCGCAAGTAATATTGCATGGTTTTCCAAAAAGGAGCCTTTTCTCTGTTCT CAACAACAAAGAATAATGAACAGATTCACTGGACTGTGAGCTTGACCATACAAGCAGAGACCAA GAAGTGGTGGTATTGATGGAGCTGCTACAACCACCACATATCTCCAAATTGACAGCATCTGATT TCCTGTCACTAGTCCCACTTCTCACAAGAGTAACTGAATTACTCGAACCTGTTAAAGTTATCAA ACCAATTTTAATGATCAATCTTGGGGCAAGGCTTTAAAAGGCACCCTCAGTGTCAATTAGAAAC ATAACATAGAGTTTCTACTGAGTCTTGGGGCAAGAGCTGTCCATCAGTGATACATTCCTCAATA CAGACATGTTCATAAGTCTGTCCAGAAGCAAAAAATGATTACCTACTCTCCATGGGCTTATATA GTTAATAGAACTAAACTTTGATAGTTGACACCAAATGCATGAACACGATCTTCATTAGAACCTT GACCAGTGAGGGAACATGGTGTTGGACACTAAGAGTCATATATCATCCAAAATTCCACTTCAGA ATAGAATGGAGTATTTTCTCATGAGGTATGACAAATAATTGATTCCTTCCGGTTGTCTTCTCCC ACACGTGCCTTGTGAATGAGTTCTTTAAAGCACGTTGCTGTCACTGCAAGTTGTCAAATTTCGT CAACTGTTGCAACCGTGCAATCATCCGATCACCAACTTCCTTCTCTGATATGGATCAAGCAACA ATGTCCAAATCTGAACAAATCACATATCAAAATTAGAATTGCAACAAGGAACTACCAGAGACCA ATTTATAAATTCAGAAGCAAATATACACGAGGGCATAATTAATCAAACTGGCTGCAAGAGACTT ATAAACCCTGAACAGTTGCTAATATCGCATGGAGGACATTGTTGCTAGCTCAACTGGGTCTCAG ATGATGTCTGTTTCAGTAAAAAGTAACACATAACTGCATTTTATCAATGGCCATAACACACAAC TTTAACAAAGCATAGAGAACAAGACCATAAAAACATAAATTACATCAAAGAACAAGAACAGAAA TCTAAAAACAAAGCAAGAAGGAGCGATCACACTTCAAATAAACCAATGAGGTAGTGGACAAAGC CCTCACCTAATTCCAGATCAAACCGGCGGAGATGACGGGTGAGGGGAAGTCAGCGCAGGATAAA CATGGGAGGGAGAGAGATAGTGGCTAAATTCCACATGGGTGACAGAGGGCGCCAAAGTATGACT TACTTGGAGTGATTTGGATAGAAAATGGTGACACGTGGACACTCAAGATATCATTTTTATCTTT TTCCCAACCACTTGTGAGCTGTGTAGGAGAGAAGTAATGAACATATAAGCAAAAACAAATGTTG TTACAAAAACAAGTCCCCACCACATTTACTACTACTAGTTTGACAAACATAAACACATTTCCCT TATTAACATTTCTTGTTAACCACACAAAGTTAATAAGTAACCCAAGTTTATACAGTTTTAAAAC ATTCTCTCTATCTCCCTCCGGCTAGGCTGTAGCTGTTCGCCATGGGAGACGCAGAGAGCACCTC CAAAACTAGCTTGCTGCTCCCGGTGGAAAGAGTTGAAAACGTGACATGGAGAGATCTGCGAGAT GGATTATTCACCGCAGAACTCAAGAGGCTTATCTGCTTTGCCGCTCCTATGGCGGCTGTTGTTA TCGCTCAGTTCATGTTGCAGATCATCTCAATGGTGATGGTTGGTCACCTCGGAAATCTCTCCCT CGCTAGTGCCTCTCTCGCCTCCTCCTTCTGCAACGTCACCGGCTTCAGCTTCATCGTCTGTTTT CTCTTCCTTCTCTCCTCTTTATCTCTATCTATTACTAGTTATCAAATTGCATCCCCTCATTACT TGATTAGTTGATTGTTACTTTTTGATGCTAGGTAGGATTGTCATGTGCCTTAGATACTTTGAGT GGTCAAGCTTATGGAGCTAAGCTATATCGGAAAGTAGGAGTTCAGACTTACACAGCAATGTTCT GTCTTGCATTAGTATGTCTCCCTCTCACTCTCATATGGTTAAACATGGAAACGCTTCTTGTATT CCTTGGCCAAGATCCTTCTATTGCTCACGAAGCCGGCAGATATGCTGCTTGCCTCATCCCAGGA CTGTTTGCTTACGCTGTTCTACAGCCTCTCACTCGCTACTTCCAAAACCAGAGCATGATTACAC CTCTCCTCATCACCTCTTGTTTTGTGTTCTGTCTCCATGTTCCTCTCTGCTGGCTTTTGGTTTA TAAGTCAGGGCTTGGTAATCTTGGAGGAGCCTTAGCTCTCAGTTTTTCGAACTGTCTTTATACC ATTATCCTTGGATCTTTAATGTGCTTCTCCTCTGCCTGTTCTGAGACACGCGCACCGCTCTCCA TGGAGATATTTGACGGCATTGGAGAGTTCTTCAGATATGCTCTTCCTTCTGCGGCTATGATTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.397055361

Conservation Information
Conserved circRNAs	NA
PMCS	0.397055361

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR846-3p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	ath-miR846-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of 1_circ_ag.3

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